MicroBridge

MicroBridge is a tool that allows file conversion between Slide annotation software like NDP.view2 to an XML format that Leica Microdissection (LMD) microscopes support.

Purpose

Scientists annotate regions of interest in software like NDP.view2, They would then have to re-draw those same annotations in the software for the LMDs.
MicroBridge takes the annotation files from NDP.view2 and converts them into a format that the LMD can understand, This gives the scientists more time to do experiments rather than annotating files for the 2nd time.

Installation

To install the package do one of the following:

A. Grab the release from the release section (Mainly for windows)

B. Clone the Repo Make a virtual environment

python3 -m venv .venv

Then:

pip install -e .

Usage

There are 2 ways to use MicroBridge Option 1: Usage via the GUI (graphical user interface) Install it first And either run

microbridge

In your terminal and it will open up Or use the desktop icon / entry to open the program

Option 2: Usage via the terminal For typical usage you would run

microbridge filename.ndpa file2.ndpa file3.ndpa ...

There are 2 flags that you can use to help with input and output Flag 1: Batch processing To process a whole folder / directory run

microbridge -b directory-path

Flag 2: output dir To set a specific directory / folder for the files be placed into run

microbridge filename.ndpa -o 'path/to/dir'

You can use both flags with each other

microbridge -b 'path/to/.ndpa/dir' -o 'path/to/output/dir'

You can also run

microbridge --help

This shows you all the commands and a quick run down of what they do

Tests

There is information about running the tests locally in the tests directory of the REPO

You can run this

python -m venv .venv
source .venv/bin/activate
pip install -e .
python run_tests.py

to set up the venv and run the tests

ndpa -> LMD(xml) example

A raw ndpa looks like this:

<!-- Calibration Point 3 - Circle annotation -->
<ndpviewstate id="3">
  <title>Calibration_3</title>
  <annotation type="circle">
    <x>200000000</x>
    <y>300000000</y>
    <radius>5000000</radius>
  </annotation>
</ndpviewstate>

<!-- RULER - should be SKIPPED -->
<ndpviewstate id="4">
  <title>Measurement_1</title>
  <annotation type="linearmeasure" displayname="AnnotateRuler" color="#ff0000">
    <x1>100000000</x1>
    <y1>100000000</y1>
    <x2>200000000</x2>
    <y2>200000000</y2>
  </annotation>
</ndpviewstate>

MicroBridge (currently) converts this to an XML for the LMD's which look like this:

  <X_CalibrationPoint_3>200000</X_CalibrationPoint_3>
  <Y_CalibrationPoint_3>300000</Y_CalibrationPoint_3>
  <ShapeCount>2</ShapeCount>
  <Shape_1>
    <PointCount>3</PointCount>
    <X_1>300000</X_1>
    <Y_1>400000</Y_1>
    <X_2>350000</X_2>
    <Y_2>400000</Y_2>
    <X_3>350000</X_3>
    <Y_3>450000</Y_3>
  </Shape_1>

This example above is cut down for length reasons

If you want to see a real world example and the full example above you can look here: ndpa --> LMD(xml) examples

Codebase Layout

src/
    ├── MicroBridge/
    │   ├── __init__.py
    │   ├── core/
    │   │   ├── __init__.py
    │   │   ├── conversion.py
    │   │   └── utils.py
    │   ├── cli/
    │   │   ├── __init__.py
    │   │   └── main.py
    │   └── gui/
    │       ├── __init__.py
    │       └── main.py
tests/
    ├── __init__.py
    ├── README.md
    ├── test_core.py
    ├── test_gui.py
    ├── test_intergration.py
    ├── test_utils.py
    ├── test_cli.py
    └── test_Data/
        └── All the test data, I am not writing that out...
        
pyproject.toml
run_tests.py

License

This project is licensed under the GNU GPLv3.0 License This is important as it support copyleft! and Free software!